Flexible Local Clock model

A BEAST 3 package for relaxed clock models within local clock models.

Time-resolved phylogenetic methods estimate evolutionary rates using dated sequence data. Standard molecular clock models assume a single substitution rate across lineages, while extensions such as local clocks and uncorrelated relaxed clocks allow structured or stochastic rate variation. The Flexible Local Clock (FLC) provides a unified framework that combines both approaches, enabling flexible modelling of rate heterogeneity across phylogenies.

Citation

Fourment M and Darling AE (2018) Local and relaxed clocks: the best of both worlds. PeerJ 6:e5140. DOI: 10.7717/peerj.5140

Maven coordinates

<dependency>
    <groupId>io.github.4ment</groupId>
    <artifactId>flc</artifactId>
    <version>1.3.0-beta1</version>
</dependency>

JPMS module name: flc

Building from source

Requires Java 25 and Maven.

mvn install -DskipTests

Running BEAST with FLC

Example:

mvn exec:exec -Dbeast.args="-overwrite examples/Human.H3.81-98-elc.xml"

License

Distributed under the GPLv3 License. See COPYING for more information.